I just returned from a conference in San Diego, where I took notes exclusively on my iPad using the Penultimate app and the Bamboo stylus from Wacom.
I bought this stylus after reading many reviews and felt it was worth the investment, especially since I planned to take notes by hand at conferences and meetings, rather than using the built-in keyboard. I purchased the Penultimate app for $.99 because of the good reviews and built-in integration with Evernote and Dropbox, for easy synching and access from other devices.
This app isn't perfect. I rest my wrist on the screen while taking notes, which can interfere with note taking because of the multitasking gestures. (These features can be turned off in Settings.) The app does allow you to select the wrist position that best reflects your writing position style, and that helped to prevent errant marks on the page from my wrist.
Before the conference, I wanted to find a note taking app that would convert handwriting to text. I only found one - Notes Plus - but it is $7.99 and I wasn't ready to spend that much money.
Overall, I'm very impressed with the Penultimate app, as well as the Bamboo stylus. I would definitely use this method again to take notes at a conference.